---
_id: '14008'
abstract:
- lang: eng
text: Time-resolved x-ray absorption spectroscopy (TR-XAS) has so far practically
been limited to large-scale facilities, to subpicosecond temporal resolution,
and to the condensed phase. We report the realization of TR-XAS with a temporal
resolution in the low femtosecond range by developing a tabletop high-harmonic
source reaching up to 350 electron volts, thus partially covering the spectral
region of 280 to 530 electron volts, where water is transmissive. We used this
source to follow previously unexamined light-induced chemical reactions in the
lowest electronic states of isolated CF4+ and SF6+ molecules in the gas phase.
By probing element-specific core-to-valence transitions at the carbon K-edge or
the sulfur L-edges, we characterized their reaction paths and observed the effect
of symmetry breaking through the splitting of absorption bands and Rydberg-valence
mixing induced by the geometry changes.
article_processing_charge: No
article_type: original
author:
- first_name: Yoann
full_name: Pertot, Yoann
last_name: Pertot
- first_name: Cédric
full_name: Schmidt, Cédric
last_name: Schmidt
- first_name: Mary
full_name: Matthews, Mary
last_name: Matthews
- first_name: Adrien
full_name: Chauvet, Adrien
last_name: Chauvet
- first_name: Martin
full_name: Huppert, Martin
last_name: Huppert
- first_name: Vit
full_name: Svoboda, Vit
last_name: Svoboda
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Andres
full_name: Tehlar, Andres
last_name: Tehlar
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Jean-Pierre
full_name: Wolf, Jean-Pierre
last_name: Wolf
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Pertot Y, Schmidt C, Matthews M, et al. Time-resolved x-ray absorption spectroscopy
with a water window high-harmonic source. Science. 2017;355(6322):264-267.
doi:10.1126/science.aah6114
apa: Pertot, Y., Schmidt, C., Matthews, M., Chauvet, A., Huppert, M., Svoboda, V.,
… Wörner, H. J. (2017). Time-resolved x-ray absorption spectroscopy with a water
window high-harmonic source. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.aah6114
chicago: Pertot, Yoann, Cédric Schmidt, Mary Matthews, Adrien Chauvet, Martin Huppert,
Vit Svoboda, Aaron von Conta, et al. “Time-Resolved x-Ray Absorption Spectroscopy
with a Water Window High-Harmonic Source.” Science. American Association
for the Advancement of Science, 2017. https://doi.org/10.1126/science.aah6114.
ieee: Y. Pertot et al., “Time-resolved x-ray absorption spectroscopy with
a water window high-harmonic source,” Science, vol. 355, no. 6322. American
Association for the Advancement of Science, pp. 264–267, 2017.
ista: Pertot Y, Schmidt C, Matthews M, Chauvet A, Huppert M, Svoboda V, von Conta
A, Tehlar A, Baykusheva DR, Wolf J-P, Wörner HJ. 2017. Time-resolved x-ray absorption
spectroscopy with a water window high-harmonic source. Science. 355(6322), 264–267.
mla: Pertot, Yoann, et al. “Time-Resolved x-Ray Absorption Spectroscopy with a Water
Window High-Harmonic Source.” Science, vol. 355, no. 6322, American Association
for the Advancement of Science, 2017, pp. 264–67, doi:10.1126/science.aah6114.
short: Y. Pertot, C. Schmidt, M. Matthews, A. Chauvet, M. Huppert, V. Svoboda, A.
von Conta, A. Tehlar, D.R. Baykusheva, J.-P. Wolf, H.J. Wörner, Science 355 (2017)
264–267.
date_created: 2023-08-10T06:36:39Z
date_published: 2017-01-05T00:00:00Z
date_updated: 2023-08-22T08:34:38Z
day: '05'
doi: 10.1126/science.aah6114
extern: '1'
external_id:
pmid:
- '28059713'
intvolume: ' 355'
issue: '6322'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa_version: None
page: 264-267
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Time-resolved x-ray absorption spectroscopy with a water window high-harmonic
source
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '14009'
abstract:
- lang: eng
text: Attosecond delays between photoelectron wave packets emitted from different
electronic shells are now well established. Is there any delay between electrons
originating from the same electronic shell but leaving the cation in different
fine-structure states? This question is relevant for all attosecond photoemission
studies involving heavy elements, be it atoms, molecules or solids. We answer
this fundamental question by measuring energy-dependent delays between photoelectron
wave packets associated with the 2P3/2 and 2P1/2 components of the electronic
groundstates of Xe+ and Kr+. We observe delays reaching up to 33±6 as in the case
of Xe. Our results are compared with two state-of-the-art theories. Whereas both
theories quantitatively agree with the results obtained for Kr, neither of them
fully reproduces the experimental results in Xe. Performing delay measurements
very close to the ionization thresholds, we compare the agreement of several analytical
formulas for the continuum-continuum delays with experimental data. Our results
show an important influence of spin-orbit coupling on attosecond photoionization
delays, highlight the requirement for additional theory development, and offer
a precision benchmark for such work.
article_number: '013404'
article_processing_charge: No
article_type: original
author:
- first_name: I.
full_name: Jordan, I.
last_name: Jordan
- first_name: M.
full_name: Huppert, M.
last_name: Huppert
- first_name: S.
full_name: Pabst, S.
last_name: Pabst
- first_name: A. S.
full_name: Kheifets, A. S.
last_name: Kheifets
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: H. J.
full_name: Wörner, H. J.
last_name: Wörner
citation:
ama: Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. Spin-orbit
delays in photoemission. Physical Review A. 2017;95(1). doi:10.1103/physreva.95.013404
apa: Jordan, I., Huppert, M., Pabst, S., Kheifets, A. S., Baykusheva, D. R., &
Wörner, H. J. (2017). Spin-orbit delays in photoemission. Physical Review A.
American Physical Society. https://doi.org/10.1103/physreva.95.013404
chicago: Jordan, I., M. Huppert, S. Pabst, A. S. Kheifets, Denitsa Rangelova Baykusheva,
and H. J. Wörner. “Spin-Orbit Delays in Photoemission.” Physical Review A.
American Physical Society, 2017. https://doi.org/10.1103/physreva.95.013404.
ieee: I. Jordan, M. Huppert, S. Pabst, A. S. Kheifets, D. R. Baykusheva, and H.
J. Wörner, “Spin-orbit delays in photoemission,” Physical Review A, vol.
95, no. 1. American Physical Society, 2017.
ista: Jordan I, Huppert M, Pabst S, Kheifets AS, Baykusheva DR, Wörner HJ. 2017.
Spin-orbit delays in photoemission. Physical Review A. 95(1), 013404.
mla: Jordan, I., et al. “Spin-Orbit Delays in Photoemission.” Physical Review
A, vol. 95, no. 1, 013404, American Physical Society, 2017, doi:10.1103/physreva.95.013404.
short: I. Jordan, M. Huppert, S. Pabst, A.S. Kheifets, D.R. Baykusheva, H.J. Wörner,
Physical Review A 95 (2017).
date_created: 2023-08-10T06:36:58Z
date_published: 2017-01-10T00:00:00Z
date_updated: 2023-08-22T08:38:17Z
day: '10'
doi: 10.1103/physreva.95.013404
extern: '1'
intvolume: ' 95'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: Physical Review A
publication_identifier:
eissn:
- 2469-9934
issn:
- 2469-9926
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Spin-orbit delays in photoemission
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 95
year: '2017'
...
---
_id: '14031'
abstract:
- lang: eng
text: High-harmonic spectroscopy driven by circularly polarized laser pulses and
their counterrotating second harmonic is a new branch of attosecond science which
currently lacks quantitative interpretations. We extend this technique to the
midinfrared regime and record detailed high-harmonic spectra of several rare-gas
atoms. These results are compared with the solution of the Schrödinger equation
in three dimensions and calculations based on the strong-field approximation that
incorporate accurate scattering-wave recombination matrix elements. A quantum-orbit
analysis of these results provides a transparent interpretation of the measured
intensity ratios of symmetry-allowed neighboring harmonics in terms of (i) a set
of propensity rules related to the angular momentum of the atomic orbitals, (ii)
atom-specific matrix elements related to their electronic structure, and (iii)
the interference of the emissions associated with electrons in orbitals corotating
or counterrotating with the laser fields. These results provide the foundation
for a quantitative understanding of bicircular high-harmonic spectroscopy.
article_number: '203201'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Simon
full_name: Brennecke, Simon
last_name: Brennecke
- first_name: Manfred
full_name: Lein, Manfred
last_name: Lein
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Baykusheva DR, Brennecke S, Lein M, Wörner HJ. Signatures of electronic structure
in bicircular high-harmonic spectroscopy. Physical Review Letters. 2017;119(20).
doi:10.1103/physrevlett.119.203201
apa: Baykusheva, D. R., Brennecke, S., Lein, M., & Wörner, H. J. (2017). Signatures
of electronic structure in bicircular high-harmonic spectroscopy. Physical
Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.119.203201
chicago: Baykusheva, Denitsa Rangelova, Simon Brennecke, Manfred Lein, and Hans
Jakob Wörner. “Signatures of Electronic Structure in Bicircular High-Harmonic
Spectroscopy.” Physical Review Letters. American Physical Society, 2017.
https://doi.org/10.1103/physrevlett.119.203201.
ieee: D. R. Baykusheva, S. Brennecke, M. Lein, and H. J. Wörner, “Signatures of
electronic structure in bicircular high-harmonic spectroscopy,” Physical Review
Letters, vol. 119, no. 20. American Physical Society, 2017.
ista: Baykusheva DR, Brennecke S, Lein M, Wörner HJ. 2017. Signatures of electronic
structure in bicircular high-harmonic spectroscopy. Physical Review Letters. 119(20),
203201.
mla: Baykusheva, Denitsa Rangelova, et al. “Signatures of Electronic Structure in
Bicircular High-Harmonic Spectroscopy.” Physical Review Letters, vol. 119,
no. 20, 203201, American Physical Society, 2017, doi:10.1103/physrevlett.119.203201.
short: D.R. Baykusheva, S. Brennecke, M. Lein, H.J. Wörner, Physical Review Letters
119 (2017).
date_created: 2023-08-10T06:48:12Z
date_published: 2017-11-17T00:00:00Z
date_updated: 2023-08-22T06:48:28Z
day: '17'
doi: 10.1103/physrevlett.119.203201
extern: '1'
external_id:
arxiv:
- '1710.04474'
pmid:
- '29219334'
intvolume: ' 119'
issue: '20'
keyword:
- General Physics and Astronomy
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1710.04474
month: '11'
oa: 1
oa_version: Preprint
pmid: 1
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Signatures of electronic structure in bicircular high-harmonic spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2017'
...
---
_id: '1407'
abstract:
- lang: eng
text: We consider the problem of computing the set of initial states of a dynamical
system such that there exists a control strategy to ensure that the trajectories
satisfy a temporal logic specification with probability 1 (almost-surely). We
focus on discrete-time, stochastic linear dynamics and specifications given as
formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over
linear predicates in the states of the system. We propose a solution based on
iterative abstraction-refinement, and turn-based 2-player probabilistic games.
While the theoretical guarantee of our algorithm after any finite number of iterations
is only a partial solution, we show that if our algorithm terminates, then the
result is the set of all satisfying initial states. Moreover, for any (partial)
solution our algorithm synthesizes witness control strategies to ensure almost-sure
satisfaction of the temporal logic specification. While the proposed algorithm
guarantees progress and soundness in every iteration, it is computationally demanding.
We offer an alternative, more efficient solution for the reachability properties
that decomposes the problem into a series of smaller problems of the same type.
All algorithms are demonstrated on an illustrative case study.
article_processing_charge: No
arxiv: 1
author:
- first_name: Mária
full_name: Svoreňová, Mária
last_name: Svoreňová
- first_name: Jan
full_name: Kretinsky, Jan
id: 44CEF464-F248-11E8-B48F-1D18A9856A87
last_name: Kretinsky
orcid: 0000-0002-8122-2881
- first_name: Martin
full_name: Chmelik, Martin
id: 3624234E-F248-11E8-B48F-1D18A9856A87
last_name: Chmelik
- first_name: Krishnendu
full_name: Chatterjee, Krishnendu
id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87
last_name: Chatterjee
orcid: 0000-0002-4561-241X
- first_name: Ivana
full_name: Cěrná, Ivana
last_name: Cěrná
- first_name: Cǎlin
full_name: Belta, Cǎlin
last_name: Belta
citation:
ama: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal
logic control for stochastic linear systems using abstraction refinement of probabilistic
games. Nonlinear Analysis: Hybrid Systems. 2017;23(2):230-253. doi:10.1016/j.nahs.2016.04.006'
apa: 'Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., &
Belta, C. (2017). Temporal logic control for stochastic linear systems using abstraction
refinement of probabilistic games. Nonlinear Analysis: Hybrid Systems.
Elsevier. https://doi.org/10.1016/j.nahs.2016.04.006'
chicago: 'Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee,
Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid
Systems. Elsevier, 2017. https://doi.org/10.1016/j.nahs.2016.04.006.'
ieee: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta,
“Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games,” Nonlinear Analysis: Hybrid Systems, vol. 23, no.
2. Elsevier, pp. 230–253, 2017.'
ista: 'Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2017.
Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games. Nonlinear Analysis: Hybrid Systems. 23(2), 230–253.'
mla: 'Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems
Using Abstraction Refinement of Probabilistic Games.” Nonlinear Analysis: Hybrid
Systems, vol. 23, no. 2, Elsevier, 2017, pp. 230–53, doi:10.1016/j.nahs.2016.04.006.'
short: 'M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta,
Nonlinear Analysis: Hybrid Systems 23 (2017) 230–253.'
date_created: 2018-12-11T11:51:50Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2025-06-11T06:33:00Z
day: '01'
department:
- _id: ToHe
- _id: KrCh
doi: 10.1016/j.nahs.2016.04.006
ec_funded: 1
external_id:
arxiv:
- '1410.5387'
isi:
- '000390637000014'
intvolume: ' 23'
isi: 1
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1410.5387
month: '02'
oa: 1
oa_version: Preprint
page: 230 - 253
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 25EE3708-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '267989'
name: Quantitative Reactive Modeling
- _id: 2581B60A-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '279307'
name: 'Quantitative Graph Games: Theory and Applications'
- _id: 25832EC2-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S 11407_N23
name: Rigorous Systems Engineering
- _id: 2584A770-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: P 23499-N23
name: Modern Graph Algorithmic Techniques in Formal Verification
- _id: 25863FF4-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: S11407
name: Game Theory
publication: 'Nonlinear Analysis: Hybrid Systems'
publication_status: published
publisher: Elsevier
publist_id: '5800'
quality_controlled: '1'
related_material:
record:
- id: '1689'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Temporal logic control for stochastic linear systems using abstraction refinement
of probabilistic games
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 23
year: '2017'
...
---
_id: '14205'
abstract:
- lang: eng
text: Two of the most fundamental prototypes of greedy optimization are the matching
pursuit and Frank-Wolfe algorithms. In this paper, we take a unified view on both
classes of methods, leading to the first explicit convergence rates of matching
pursuit methods in an optimization sense, for general sets of atoms. We derive
sublinear (1/t) convergence for both classes on general smooth objectives, and
linear convergence on strongly convex objectives, as well as a clear correspondence
of algorithm variants. Our presented algorithms and rates are affine invariant,
and do not need any incoherence or sparsity assumptions.
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Rajiv
full_name: Khanna, Rajiv
last_name: Khanna
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Khanna R, Tschannen M, Jaggi M. A unified optimization view on
generalized matching pursuit and Frank-Wolfe. In: Proceedings of the 20th International
Conference on Artificial Intelligence and Statistics. Vol 54. ML Research
Press; 2017:860-868.'
apa: 'Locatello, F., Khanna, R., Tschannen, M., & Jaggi, M. (2017). A unified
optimization view on generalized matching pursuit and Frank-Wolfe. In Proceedings
of the 20th International Conference on Artificial Intelligence and Statistics
(Vol. 54, pp. 860–868). Fort Lauderdale, FL, United States: ML Research Press.'
chicago: Locatello, Francesco, Rajiv Khanna, Michael Tschannen, and Martin Jaggi.
“A Unified Optimization View on Generalized Matching Pursuit and Frank-Wolfe.”
In Proceedings of the 20th International Conference on Artificial Intelligence
and Statistics, 54:860–68. ML Research Press, 2017.
ieee: F. Locatello, R. Khanna, M. Tschannen, and M. Jaggi, “A unified optimization
view on generalized matching pursuit and Frank-Wolfe,” in Proceedings of the
20th International Conference on Artificial Intelligence and Statistics, Fort
Lauderdale, FL, United States, 2017, vol. 54, pp. 860–868.
ista: 'Locatello F, Khanna R, Tschannen M, Jaggi M. 2017. A unified optimization
view on generalized matching pursuit and Frank-Wolfe. Proceedings of the 20th
International Conference on Artificial Intelligence and Statistics. AISTATS: Conference
on Artificial Intelligence and Statistics vol. 54, 860–868.'
mla: Locatello, Francesco, et al. “A Unified Optimization View on Generalized Matching
Pursuit and Frank-Wolfe.” Proceedings of the 20th International Conference
on Artificial Intelligence and Statistics, vol. 54, ML Research Press, 2017,
pp. 860–68.
short: F. Locatello, R. Khanna, M. Tschannen, M. Jaggi, in:, Proceedings of the
20th International Conference on Artificial Intelligence and Statistics, ML Research
Press, 2017, pp. 860–868.
conference:
end_date: 2017-04-22
location: Fort Lauderdale, FL, United States
name: 'AISTATS: Conference on Artificial Intelligence and Statistics'
start_date: 2017-04-20
date_created: 2023-08-22T14:17:19Z
date_published: 2017-02-21T00:00:00Z
date_updated: 2023-09-13T09:49:10Z
day: '21'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1702.06457'
intvolume: ' 54'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1702.06457
month: '02'
oa: 1
oa_version: Preprint
page: 860-868
publication: Proceedings of the 20th International Conference on Artificial Intelligence
and Statistics
publication_status: published
publisher: ML Research Press
quality_controlled: '1'
status: public
title: A unified optimization view on generalized matching pursuit and Frank-Wolfe
type: conference
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 54
year: '2017'
...
---
_id: '14206'
abstract:
- lang: eng
text: Greedy optimization methods such as Matching Pursuit (MP) and Frank-Wolfe
(FW) algorithms regained popularity in recent years due to their simplicity, effectiveness
and theoretical guarantees. MP and FW address optimization over the linear span
and the convex hull of a set of atoms, respectively. In this paper, we consider
the intermediate case of optimization over the convex cone, parametrized as the
conic hull of a generic atom set, leading to the first principled definitions
of non-negative MP algorithms for which we give explicit convergence rates and
demonstrate excellent empirical performance. In particular, we derive sublinear
(O(1/t)) convergence on general smooth and convex objectives, and linear convergence
(O(e−t)) on strongly convex objectives, in both cases for general sets of atoms.
Furthermore, we establish a clear correspondence of our algorithms to known algorithms
from the MP and FW literature. Our novel algorithms and analyses target general
atom sets and general objective functions, and hence are directly applicable to
a large variety of learning settings.
article_processing_charge: No
arxiv: 1
author:
- first_name: Francesco
full_name: Locatello, Francesco
id: 26cfd52f-2483-11ee-8040-88983bcc06d4
last_name: Locatello
orcid: 0000-0002-4850-0683
- first_name: Michael
full_name: Tschannen, Michael
last_name: Tschannen
- first_name: Gunnar
full_name: Rätsch, Gunnar
last_name: Rätsch
- first_name: Martin
full_name: Jaggi, Martin
last_name: Jaggi
citation:
ama: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. Greedy algorithms for cone constrained
optimization with convergence guarantees. In: Advances in Neural Information
Processing Systems. ; 2017.'
apa: Locatello, F., Tschannen, M., Rätsch, G., & Jaggi, M. (2017). Greedy algorithms
for cone constrained optimization with convergence guarantees. In Advances
in Neural Information Processing Systems. Long Beach, CA, United States.
chicago: Locatello, Francesco, Michael Tschannen, Gunnar Rätsch, and Martin Jaggi.
“Greedy Algorithms for Cone Constrained Optimization with Convergence Guarantees.”
In Advances in Neural Information Processing Systems, 2017.
ieee: F. Locatello, M. Tschannen, G. Rätsch, and M. Jaggi, “Greedy algorithms for
cone constrained optimization with convergence guarantees,” in Advances in
Neural Information Processing Systems, Long Beach, CA, United States, 2017.
ista: 'Locatello F, Tschannen M, Rätsch G, Jaggi M. 2017. Greedy algorithms for
cone constrained optimization with convergence guarantees. Advances in Neural
Information Processing Systems. NeurIPS: Neural Information Processing Systems.'
mla: Locatello, Francesco, et al. “Greedy Algorithms for Cone Constrained Optimization
with Convergence Guarantees.” Advances in Neural Information Processing Systems,
2017.
short: F. Locatello, M. Tschannen, G. Rätsch, M. Jaggi, in:, Advances in Neural
Information Processing Systems, 2017.
conference:
end_date: 2017-12-09
location: Long Beach, CA, United States
name: 'NeurIPS: Neural Information Processing Systems'
start_date: 2017-12-04
date_created: 2023-08-22T14:17:38Z
date_published: 2017-05-31T00:00:00Z
date_updated: 2024-10-14T12:29:50Z
day: '31'
department:
- _id: FrLo
extern: '1'
external_id:
arxiv:
- '1705.11041'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1705.11041
month: '05'
oa: 1
oa_version: Preprint
publication: Advances in Neural Information Processing Systems
publication_identifier:
isbn:
- '9781510860964'
publication_status: published
quality_controlled: '1'
status: public
title: Greedy algorithms for cone constrained optimization with convergence guarantees
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
_id: '14286'
abstract:
- lang: eng
text: 'The bacteriophage M13 has found frequent applications in nanobiotechnology
due to its chemically and genetically tunable protein surface and its ability
to self-assemble into colloidal membranes. Additionally, its single-stranded (ss)
genome is commonly used as scaffold for DNA origami. Despite the manifold uses
of M13, upstream production methods for phage and scaffold ssDNA are underexamined
with respect to future industrial usage. Here, the high-cell-density phage production
with Escherichia coli as host organism was studied in respect of medium composition,
infection time, multiplicity of infection, and specific growth rate. The specific
growth rate and the multiplicity of infection were identified as the crucial state
variables that influence phage amplification rate on one hand and the concentration
of produced ssDNA on the other hand. Using a growth rate of 0.15 h−1 and a multiplicity
of infection of 0.05 pfu cfu−1 in the fed-batch production process, the concentration
of pure isolated M13 ssDNA usable for scaffolded DNA origami could be enhanced
by 54% to 590 mg L−1. Thus, our results help enabling M13 production for industrial
uses in nanobiotechnology. Biotechnol. Bioeng. 2017;114: 777–784.'
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin
full_name: Kick, Benjamin
last_name: Kick
- first_name: Samantha
full_name: Hensler, Samantha
last_name: Hensler
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Dirk
full_name: Weuster-Botz, Dirk
last_name: Weuster-Botz
citation:
ama: Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. Specific growth
rate and multiplicity of infection affect high-cell-density fermentation with
bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering.
2017;114(4):777-784. doi:10.1002/bit.26200
apa: Kick, B., Hensler, S., Praetorius, F. M., Dietz, H., & Weuster-Botz, D.
(2017). Specific growth rate and multiplicity of infection affect high-cell-density
fermentation with bacteriophage M13 for ssDNA production. Biotechnology and
Bioengineering. Wiley. https://doi.org/10.1002/bit.26200
chicago: Kick, Benjamin, Samantha Hensler, Florian M Praetorius, Hendrik Dietz,
and Dirk Weuster-Botz. “Specific Growth Rate and Multiplicity of Infection Affect
High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.” Biotechnology
and Bioengineering. Wiley, 2017. https://doi.org/10.1002/bit.26200.
ieee: B. Kick, S. Hensler, F. M. Praetorius, H. Dietz, and D. Weuster-Botz, “Specific
growth rate and multiplicity of infection affect high-cell-density fermentation
with bacteriophage M13 for ssDNA production,” Biotechnology and Bioengineering,
vol. 114, no. 4. Wiley, pp. 777–784, 2017.
ista: Kick B, Hensler S, Praetorius FM, Dietz H, Weuster-Botz D. 2017. Specific
growth rate and multiplicity of infection affect high-cell-density fermentation
with bacteriophage M13 for ssDNA production. Biotechnology and Bioengineering.
114(4), 777–784.
mla: Kick, Benjamin, et al. “Specific Growth Rate and Multiplicity of Infection
Affect High-Cell-Density Fermentation with Bacteriophage M13 for SsDNA Production.”
Biotechnology and Bioengineering, vol. 114, no. 4, Wiley, 2017, pp. 777–84,
doi:10.1002/bit.26200.
short: B. Kick, S. Hensler, F.M. Praetorius, H. Dietz, D. Weuster-Botz, Biotechnology
and Bioengineering 114 (2017) 777–784.
date_created: 2023-09-06T12:08:29Z
date_published: 2017-04-01T00:00:00Z
date_updated: 2023-11-07T12:36:20Z
day: '01'
doi: 10.1002/bit.26200
extern: '1'
external_id:
pmid:
- '27748519'
intvolume: ' 114'
issue: '4'
keyword:
- Applied Microbiology and Biotechnology
- Bioengineering
- Biotechnology
language:
- iso: eng
month: '04'
oa_version: None
page: 777-784
pmid: 1
publication: Biotechnology and Bioengineering
publication_identifier:
issn:
- 0006-3592
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: Specific growth rate and multiplicity of infection affect high-cell-density
fermentation with bacteriophage M13 for ssDNA production
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '14287'
abstract:
- lang: eng
text: We describe an approach to bottom-up fabrication that allows integration of
the functional diversity of proteins into designed three-dimensional structural
frameworks. A set of custom staple proteins based on transcription activator–like
effector proteins folds a double-stranded DNA template into a user-defined shape.
Each staple protein is designed to recognize and closely link two distinct double-helical
DNA sequences at separate positions on the template. We present design rules for
constructing megadalton-scale DNA-protein hybrid shapes; introduce various structural
motifs, such as custom curvature, corners, and vertices; and describe principles
for creating multilayer DNA-protein objects with enhanced rigidity. We demonstrate
self-assembly of our hybrid nanostructures in one-pot mixtures that include the
genetic information for the designed proteins, the template DNA, RNA polymerase,
ribosomes, and cofactors for transcription and translation.
article_number: eaam5488
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Praetorius FM, Dietz H. Self-assembly of genetically encoded DNA-protein hybrid
nanoscale shapes. Science. 2017;355(6331). doi:10.1126/science.aam5488
apa: Praetorius, F. M., & Dietz, H. (2017). Self-assembly of genetically encoded
DNA-protein hybrid nanoscale shapes. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aam5488
chicago: Praetorius, Florian M, and Hendrik Dietz. “Self-Assembly of Genetically
Encoded DNA-Protein Hybrid Nanoscale Shapes.” Science. American Association
for the Advancement of Science, 2017. https://doi.org/10.1126/science.aam5488.
ieee: F. M. Praetorius and H. Dietz, “Self-assembly of genetically encoded DNA-protein
hybrid nanoscale shapes,” Science, vol. 355, no. 6331. American Association
for the Advancement of Science, 2017.
ista: Praetorius FM, Dietz H. 2017. Self-assembly of genetically encoded DNA-protein
hybrid nanoscale shapes. Science. 355(6331), eaam5488.
mla: Praetorius, Florian M., and Hendrik Dietz. “Self-Assembly of Genetically Encoded
DNA-Protein Hybrid Nanoscale Shapes.” Science, vol. 355, no. 6331, eaam5488,
American Association for the Advancement of Science, 2017, doi:10.1126/science.aam5488.
short: F.M. Praetorius, H. Dietz, Science 355 (2017).
date_created: 2023-09-06T12:08:55Z
date_published: 2017-03-24T00:00:00Z
date_updated: 2023-11-07T12:33:05Z
day: '24'
doi: 10.1126/science.aam5488
extern: '1'
external_id:
pmid:
- '28336611'
intvolume: ' 355'
issue: '6331'
language:
- iso: eng
month: '03'
oa_version: None
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Self-assembly of genetically encoded DNA-protein hybrid nanoscale shapes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '14290'
abstract:
- lang: eng
text: DNA nanotechnology, in particular DNA origami, enables the bottom-up self-assembly
of micrometre-scale, three-dimensional structures with nanometre-precise features1,2,3,4,5,6,7,8,9,10,11,12.
These structures are customizable in that they can be site-specifically functionalized13
or constructed to exhibit machine-like14,15 or logic-gating behaviour16. Their
use has been limited to applications that require only small amounts of material
(of the order of micrograms), owing to the limitations of current production methods.
But many proposed applications, for example as therapeutic agents or in complex
materials3,16,17,18,19,20,21,22, could be realized if more material could be used.
In DNA origami, a nanostructure is assembled from a very long single-stranded
scaffold molecule held in place by many short single-stranded staple oligonucleotides.
Only the bacteriophage-derived scaffold molecules are amenable to scalable and
efficient mass production23; the shorter staple strands are obtained through costly
solid-phase synthesis24 or enzymatic processes25. Here we show that single strands
of DNA of virtually arbitrary length and with virtually arbitrary sequences can
be produced in a scalable and cost-efficient manner by using bacteriophages to
generate single-stranded precursor DNA that contains target strand sequences interleaved
with self-excising ‘cassettes’, with each cassette comprising two Zn2+-dependent
DNA-cleaving DNA enzymes. We produce all of the necessary single strands of DNA
for several DNA origami using shaker-flask cultures, and demonstrate end-to-end
production of macroscopic amounts of a DNA origami nanorod in a litre-scale stirred-tank
bioreactor. Our method is compatible with existing DNA origami design frameworks
and retains the modularity and addressability of DNA origami objects that are
necessary for implementing custom modifications using functional groups. With
all of the production and purification steps amenable to scaling, we expect that
our method will expand the scope of DNA nanotechnology in many areas of science
and technology.
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Benjamin
full_name: Kick, Benjamin
last_name: Kick
- first_name: Karl L.
full_name: Behler, Karl L.
last_name: Behler
- first_name: Maximilian N.
full_name: Honemann, Maximilian N.
last_name: Honemann
- first_name: Dirk
full_name: Weuster-Botz, Dirk
last_name: Weuster-Botz
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. Biotechnological
mass production of DNA origami. Nature. 2017;552(7683):84-87. doi:10.1038/nature24650
apa: Praetorius, F. M., Kick, B., Behler, K. L., Honemann, M. N., Weuster-Botz,
D., & Dietz, H. (2017). Biotechnological mass production of DNA origami. Nature.
Springer Nature. https://doi.org/10.1038/nature24650
chicago: Praetorius, Florian M, Benjamin Kick, Karl L. Behler, Maximilian N. Honemann,
Dirk Weuster-Botz, and Hendrik Dietz. “Biotechnological Mass Production of DNA
Origami.” Nature. Springer Nature, 2017. https://doi.org/10.1038/nature24650.
ieee: F. M. Praetorius, B. Kick, K. L. Behler, M. N. Honemann, D. Weuster-Botz,
and H. Dietz, “Biotechnological mass production of DNA origami,” Nature,
vol. 552, no. 7683. Springer Nature, pp. 84–87, 2017.
ista: Praetorius FM, Kick B, Behler KL, Honemann MN, Weuster-Botz D, Dietz H. 2017.
Biotechnological mass production of DNA origami. Nature. 552(7683), 84–87.
mla: Praetorius, Florian M., et al. “Biotechnological Mass Production of DNA Origami.”
Nature, vol. 552, no. 7683, Springer Nature, 2017, pp. 84–87, doi:10.1038/nature24650.
short: F.M. Praetorius, B. Kick, K.L. Behler, M.N. Honemann, D. Weuster-Botz, H.
Dietz, Nature 552 (2017) 84–87.
date_created: 2023-09-06T12:14:20Z
date_published: 2017-12-07T00:00:00Z
date_updated: 2023-11-07T12:24:49Z
day: '07'
doi: 10.1038/nature24650
extern: '1'
external_id:
pmid:
- '29219963'
intvolume: ' 552'
issue: '7683'
language:
- iso: eng
month: '12'
oa_version: None
page: 84-87
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Biotechnological mass production of DNA origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 552
year: '2017'
...
---
_id: '14308'
abstract:
- lang: eng
text: Here we describe an approach to bottom-up fabrication with nanometer-precision
that allows integrating the functional diversity of proteins in designed three-dimensional
structural frameworks. We reimagined the successful DNA origami design principle
using a set of custom staple proteins to fold a double-stranded DNA template into
a user-defined shape. Each staple protein recognizes two distinct double-helical
DNA sequences and can carry additional functionalities. The staple proteins we
present here are based on the transcription activator-like (TAL) effector proteins.
Due to their repetitive structure these proteins offer a unique programmability
that enables us to construct numerous staple proteins targeting any desired DNA
sequence. Our approach is general, meaning that many different objects may be
created using the same set of rules, and it is modular, because components can
be modified or exchanged individually. We present rules for constructing megadalton-scale
DNA-protein hybrid nanostructures; introduce important structural motifs, such
as curvature, corners, and vertices; describe principles for creating multi-layer
DNA-protein objects with enhanced rigidity; and demonstrate the possibility to
combine our DNA-protein hybrid origami with conventional DNA nanotechnology. Since
all components can be encoded genetically, our structures should be amenable to
biotechnological mass-production. Moreover, since the target objects can self-assemble
at room temperature in near-physiological buffer, our hybrid origami may also
provide an attractive method to realize positioning and scaffolding tasks in vivo.
We expect our method to find application both in scaffolding protein functionalities
and in manipulating the spatial arrangement of genomic DNA.
article_number: 25a
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
citation:
ama: Praetorius FM, Dietz H. Genetically encoded DNA-protein hybrid origami. Biophysical
Journal. 2017;112(3). doi:10.1016/j.bpj.2016.11.171
apa: Praetorius, F. M., & Dietz, H. (2017). Genetically encoded DNA-protein
hybrid origami. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2016.11.171
chicago: Praetorius, Florian M, and Hendrik Dietz. “Genetically Encoded DNA-Protein
Hybrid Origami.” Biophysical Journal. Elsevier, 2017. https://doi.org/10.1016/j.bpj.2016.11.171.
ieee: F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,”
Biophysical Journal, vol. 112, no. 3. Elsevier, 2017.
ista: Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami.
Biophysical Journal. 112(3), 25a.
mla: Praetorius, Florian M., and Hendrik Dietz. “Genetically Encoded DNA-Protein
Hybrid Origami.” Biophysical Journal, vol. 112, no. 3, 25a, Elsevier, 2017,
doi:10.1016/j.bpj.2016.11.171.
short: F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).
date_created: 2023-09-06T13:19:10Z
date_published: 2017-02-03T00:00:00Z
date_updated: 2024-10-14T12:31:35Z
day: '03'
doi: 10.1016/j.bpj.2016.11.171
extern: '1'
intvolume: ' 112'
issue: '3'
keyword:
- Biophysics
language:
- iso: eng
month: '02'
oa_version: None
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetically encoded DNA-protein hybrid origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2017'
...
---
_id: '14309'
abstract:
- lang: eng
text: Establishing precise control over the shape and the interactions of the microscopic
building blocks is essential for design of macroscopic soft materials with novel
structural, optical and mechanical properties. Here, we demonstrate robust assembly
of DNA origami filaments into cholesteric liquid crystals, one-dimensional supramolecular
twisted ribbons and two-dimensional colloidal membranes. The exquisite control
afforded by the DNA origami technology establishes a quantitative relationship
between the microscopic filament structure and the macroscopic cholesteric pitch.
Furthermore, it also enables robust assembly of one-dimensional twisted ribbons,
which behave as effective supramolecular polymers whose structure and elastic
properties can be precisely tuned by controlling the geometry of the elemental
building blocks. Our results demonstrate the potential synergy between DNA origami
technology and colloidal science, in which the former allows for rapid and robust
synthesis of complex particles, and the latter can be used to assemble such particles
into bulk materials.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: M
full_name: Siavashpouri, M
last_name: Siavashpouri
- first_name: CH
full_name: Wachauf, CH
last_name: Wachauf
- first_name: MJ
full_name: Zakhary, MJ
last_name: Zakhary
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: H
full_name: Dietz, H
last_name: Dietz
- first_name: Z
full_name: Dogic, Z
last_name: Dogic
citation:
ama: Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular
engineering of chiral colloidal liquid crystals using DNA origami. Nature Materials.
2017;16(8):849-856. doi:10.1038/nmat4909
apa: Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &
Dogic, Z. (2017). Molecular engineering of chiral colloidal liquid crystals using
DNA origami. Nature Materials. Springer Nature. https://doi.org/10.1038/nmat4909
chicago: Siavashpouri, M, CH Wachauf, MJ Zakhary, Florian M Praetorius, H Dietz,
and Z Dogic. “Molecular Engineering of Chiral Colloidal Liquid Crystals Using
DNA Origami.” Nature Materials. Springer Nature, 2017. https://doi.org/10.1038/nmat4909.
ieee: M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z.
Dogic, “Molecular engineering of chiral colloidal liquid crystals using DNA origami,”
Nature Materials, vol. 16, no. 8. Springer Nature, pp. 849–856, 2017.
ista: Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017.
Molecular engineering of chiral colloidal liquid crystals using DNA origami. Nature
Materials. 16(8), 849–856.
mla: Siavashpouri, M., et al. “Molecular Engineering of Chiral Colloidal Liquid
Crystals Using DNA Origami.” Nature Materials, vol. 16, no. 8, Springer
Nature, 2017, pp. 849–56, doi:10.1038/nmat4909.
short: M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic,
Nature Materials 16 (2017) 849–856.
date_created: 2023-09-06T13:37:27Z
date_published: 2017-05-22T00:00:00Z
date_updated: 2023-11-07T11:40:00Z
day: '22'
doi: 10.1038/nmat4909
extern: '1'
external_id:
arxiv:
- '1705.08944'
pmid:
- '28530665'
intvolume: ' 16'
issue: '8'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.1705.08944'
month: '05'
oa: 1
oa_version: Preprint
page: 849-856
pmid: 1
publication: Nature Materials
publication_identifier:
eissn:
- 1476-4660
issn:
- 1476-1122
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Molecular engineering of chiral colloidal liquid crystals using DNA origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2017'
...
---
_id: '14310'
article_processing_charge: No
author:
- first_name: Mahsa
full_name: Siavashpouri, Mahsa
last_name: Siavashpouri
- first_name: Christian
full_name: Wachauf, Christian
last_name: Wachauf
- first_name: Mark
full_name: Zakhary, Mark
last_name: Zakhary
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Zvonimir
full_name: Dogic, Zvonimir
last_name: Dogic
citation:
ama: 'Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. Molecular
engineering of colloidal liquid crystals using DNA origami. In: APS March Meeting
2017. APS; 2017.'
apa: Siavashpouri, M., Wachauf, C., Zakhary, M., Praetorius, F. M., Dietz, H., &
Dogic, Z. (2017). Molecular engineering of colloidal liquid crystals using DNA
origami. In APS March Meeting 2017. APS.
chicago: Siavashpouri, Mahsa, Christian Wachauf, Mark Zakhary, Florian M Praetorius,
Hendrik Dietz, and Zvonimir Dogic. “Molecular Engineering of Colloidal Liquid
Crystals Using DNA Origami.” In APS March Meeting 2017. APS, 2017.
ieee: M. Siavashpouri, C. Wachauf, M. Zakhary, F. M. Praetorius, H. Dietz, and Z.
Dogic, “Molecular engineering of colloidal liquid crystals using DNA origami,”
in APS March Meeting 2017, 2017.
ista: Siavashpouri M, Wachauf C, Zakhary M, Praetorius FM, Dietz H, Dogic Z. 2017.
Molecular engineering of colloidal liquid crystals using DNA origami. APS March
Meeting 2017. .
mla: Siavashpouri, Mahsa, et al. “Molecular Engineering of Colloidal Liquid Crystals
Using DNA Origami.” APS March Meeting 2017, APS, 2017.
short: M. Siavashpouri, C. Wachauf, M. Zakhary, F.M. Praetorius, H. Dietz, Z. Dogic,
in:, APS March Meeting 2017, APS, 2017.
date_created: 2023-09-06T13:40:20Z
date_published: 2017-03-01T00:00:00Z
date_updated: 2023-11-07T11:36:15Z
day: '01'
extern: '1'
language:
- iso: eng
month: '03'
oa_version: None
publication: APS March Meeting 2017
publication_status: published
publisher: APS
quality_controlled: '1'
status: public
title: Molecular engineering of colloidal liquid crystals using DNA origami
type: conference_abstract
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2017'
...
---
OA_type: free access
_id: '1433'
abstract:
- lang: eng
text: Phat is an open-source C. ++ library for the computation of persistent homology
by matrix reduction, targeted towards developers of software for topological data
analysis. We aim for a simple generic design that decouples algorithms from data
structures without sacrificing efficiency or user-friendliness. We provide numerous
different reduction strategies as well as data types to store and manipulate the
boundary matrix. We compare the different combinations through extensive experimental
evaluation and identify optimization techniques that work well in practical situations.
We also compare our software with various other publicly available libraries for
persistent homology.
acknowledgement: Michael Kerber acknowledges support by the Max Planck Center for
Visual Computing and Communications (FKZ-01IMC01 and FKZ-01IM10001). Ulrich Bauer,
Jan Reininghaus, and Hubert Wagner acknowledge support by the EU Project TOPOSYS
(FP7-ICT-318493-STREP).
article_processing_charge: No
article_type: original
author:
- first_name: Ulrich
full_name: Bauer, Ulrich
last_name: Bauer
- first_name: Michael
full_name: Kerber, Michael
last_name: Kerber
- first_name: Jan
full_name: Reininghaus, Jan
last_name: Reininghaus
- first_name: Hubert
full_name: Wagner, Hubert
id: 379CA8B8-F248-11E8-B48F-1D18A9856A87
last_name: Wagner
orcid: 0009-0009-9111-8429
citation:
ama: Bauer U, Kerber M, Reininghaus J, Wagner H. Phat - Persistent homology algorithms
toolbox. Journal of Symbolic Computation. 2017;78:76-90. doi:10.1016/j.jsc.2016.03.008
apa: Bauer, U., Kerber, M., Reininghaus, J., & Wagner, H. (2017). Phat - Persistent
homology algorithms toolbox. Journal of Symbolic Computation. Academic
Press. https://doi.org/10.1016/j.jsc.2016.03.008
chicago: Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “Phat
- Persistent Homology Algorithms Toolbox.” Journal of Symbolic Computation.
Academic Press, 2017. https://doi.org/10.1016/j.jsc.2016.03.008.
ieee: U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “Phat - Persistent homology
algorithms toolbox,” Journal of Symbolic Computation, vol. 78. Academic
Press, pp. 76–90, 2017.
ista: Bauer U, Kerber M, Reininghaus J, Wagner H. 2017. Phat - Persistent homology
algorithms toolbox. Journal of Symbolic Computation. 78, 76–90.
mla: Bauer, Ulrich, et al. “Phat - Persistent Homology Algorithms Toolbox.” Journal
of Symbolic Computation, vol. 78, Academic Press, 2017, pp. 76–90, doi:10.1016/j.jsc.2016.03.008.
short: U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, Journal of Symbolic Computation
78 (2017) 76–90.
corr_author: '1'
date_created: 2018-12-11T11:51:59Z
date_published: 2017-01-01T00:00:00Z
date_updated: 2026-06-18T17:35:16Z
day: '01'
ddc:
- '500'
department:
- _id: HeEd
doi: 10.1016/j.jsc.2016.03.008
ec_funded: 1
external_id:
isi:
- '000384396000005'
intvolume: ' 78'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.jsc.2016.03.008
month: '01'
oa: 1
oa_version: Published Version
page: 76 - 90
project:
- _id: 255D761E-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '318493'
name: Topological Complex Systems
publication: Journal of Symbolic Computation
publication_identifier:
issn:
- ' 0747-7171'
publication_status: published
publisher: Academic Press
publist_id: '5765'
quality_controlled: '1'
related_material:
record:
- id: '10894'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Phat - Persistent homology algorithms toolbox
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 78
year: '2017'
...
---
_id: '15154'
abstract:
- lang: eng
text: Biofilm formation is critical for the infection cycle of Vibrio cholerae.
Vibrio exopolysaccharides (VPS) and the matrix proteins RbmA, Bap1 and RbmC are
required for the development of biofilm architecture. We demonstrate that RbmA
binds VPS directly and uses a binary structural switch within its first fibronectin
type III (FnIII-1) domain to control RbmA structural dynamics and the formation
of VPS-dependent higher-order structures. The structural switch in FnIII-1 regulates
interactions in trans with the FnIII-2 domain, leading to open (monomeric) or
closed (dimeric) interfaces. The ability of RbmA to switch between open and closed
states is important for V. cholerae biofilm formation, as RbmA variants with switches
that are locked in either of the two states lead to biofilms with altered architecture
and structural integrity.
article_number: '26163'
article_processing_charge: Yes
article_type: original
author:
- first_name: Jiunn CN
full_name: Fong, Jiunn CN
last_name: Fong
- first_name: Andrew
full_name: Rogers, Andrew
last_name: Rogers
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Nicole C
full_name: Parsley, Nicole C
last_name: Parsley
- first_name: William-Cole
full_name: Cornell, William-Cole
last_name: Cornell
- first_name: Yu-Cheng
full_name: Lin, Yu-Cheng
last_name: Lin
- first_name: Praveen K
full_name: Singh, Praveen K
last_name: Singh
- first_name: Raimo
full_name: Hartmann, Raimo
last_name: Hartmann
- first_name: Knut
full_name: Drescher, Knut
last_name: Drescher
- first_name: Evgeny
full_name: Vinogradov, Evgeny
last_name: Vinogradov
- first_name: Lars EP
full_name: Dietrich, Lars EP
last_name: Dietrich
- first_name: Carrie L
full_name: Partch, Carrie L
last_name: Partch
- first_name: Fitnat H
full_name: Yildiz, Fitnat H
last_name: Yildiz
citation:
ama: Fong JC, Rogers A, Michael AK, et al. Structural dynamics of RbmA governs plasticity
of Vibrio cholerae biofilms. eLife. 2017;6. doi:10.7554/elife.26163
apa: Fong, J. C., Rogers, A., Michael, A. K., Parsley, N. C., Cornell, W.-C., Lin,
Y.-C., … Yildiz, F. H. (2017). Structural dynamics of RbmA governs plasticity
of Vibrio cholerae biofilms. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.26163
chicago: Fong, Jiunn CN, Andrew Rogers, Alicia K. Michael, Nicole C Parsley, William-Cole
Cornell, Yu-Cheng Lin, Praveen K Singh, et al. “Structural Dynamics of RbmA Governs
Plasticity of Vibrio Cholerae Biofilms.” ELife. eLife Sciences Publications,
2017. https://doi.org/10.7554/elife.26163.
ieee: J. C. Fong et al., “Structural dynamics of RbmA governs plasticity
of Vibrio cholerae biofilms,” eLife, vol. 6. eLife Sciences Publications,
2017.
ista: Fong JC, Rogers A, Michael AK, Parsley NC, Cornell W-C, Lin Y-C, Singh PK,
Hartmann R, Drescher K, Vinogradov E, Dietrich LE, Partch CL, Yildiz FH. 2017.
Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms. eLife.
6, 26163.
mla: Fong, Jiunn CN, et al. “Structural Dynamics of RbmA Governs Plasticity of Vibrio
Cholerae Biofilms.” ELife, vol. 6, 26163, eLife Sciences Publications,
2017, doi:10.7554/elife.26163.
short: J.C. Fong, A. Rogers, A.K. Michael, N.C. Parsley, W.-C. Cornell, Y.-C. Lin,
P.K. Singh, R. Hartmann, K. Drescher, E. Vinogradov, L.E. Dietrich, C.L. Partch,
F.H. Yildiz, ELife 6 (2017).
date_created: 2024-03-21T07:55:36Z
date_published: 2017-08-01T00:00:00Z
date_updated: 2024-03-25T12:22:54Z
day: '01'
doi: 10.7554/elife.26163
extern: '1'
external_id:
pmid:
- '28762945'
intvolume: ' 6'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.7554/eLife.26163
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural dynamics of RbmA governs plasticity of Vibrio cholerae biofilms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 6
year: '2017'
...
---
_id: '15155'
abstract:
- lang: eng
text: The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like
1) is a regulatory hub for transcriptional coactivators and repressors that compete
for binding and, consequently, contributes to period determination of the mammalian
circadian clock. Here, we report the discovery of two distinct conformational
states that slowly exchange within the dynamic TAD to control timing. This binary
switch results from cis/trans isomerization about a highly conserved Trp-Pro imide
bond in a region of the TAD that is required for normal circadian timekeeping.
Both cis and trans isomers interact with transcriptional regulators, suggesting
that isomerization could serve a role in assembling regulatory complexes in vivo.
Toward this end, we show that locking the switch into the trans isomer leads to
shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin
family of peptidyl-prolyl isomerases, highlighting the potential for regulation
of BMAL1 protein dynamics in period determination.
article_processing_charge: No
article_type: original
author:
- first_name: Chelsea L.
full_name: Gustafson, Chelsea L.
last_name: Gustafson
- first_name: Nicole C.
full_name: Parsley, Nicole C.
last_name: Parsley
- first_name: Hande
full_name: Asimgil, Hande
last_name: Asimgil
- first_name: Hsiau-Wei
full_name: Lee, Hsiau-Wei
last_name: Lee
- first_name: Christopher
full_name: Ahlbach, Christopher
last_name: Ahlbach
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Haiyan
full_name: Xu, Haiyan
last_name: Xu
- first_name: Owen L.
full_name: Williams, Owen L.
last_name: Williams
- first_name: Tara L.
full_name: Davis, Tara L.
last_name: Davis
- first_name: Andrew C.
full_name: Liu, Andrew C.
last_name: Liu
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Gustafson CL, Parsley NC, Asimgil H, et al. A slow conformational switch in
the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell.
2017;66(4):447-457.e7. doi:10.1016/j.molcel.2017.04.011
apa: Gustafson, C. L., Parsley, N. C., Asimgil, H., Lee, H.-W., Ahlbach, C., Michael,
A. K., … Partch, C. L. (2017). A slow conformational switch in the BMAL1 transactivation
domain modulates circadian rhythms. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2017.04.011
chicago: Gustafson, Chelsea L., Nicole C. Parsley, Hande Asimgil, Hsiau-Wei Lee,
Christopher Ahlbach, Alicia K. Michael, Haiyan Xu, et al. “A Slow Conformational
Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.” Molecular
Cell. Elsevier, 2017. https://doi.org/10.1016/j.molcel.2017.04.011.
ieee: C. L. Gustafson et al., “A slow conformational switch in the BMAL1
transactivation domain modulates circadian rhythms,” Molecular Cell, vol.
66, no. 4. Elsevier, p. 447–457.e7, 2017.
ista: Gustafson CL, Parsley NC, Asimgil H, Lee H-W, Ahlbach C, Michael AK, Xu H,
Williams OL, Davis TL, Liu AC, Partch CL. 2017. A slow conformational switch in
the BMAL1 transactivation domain modulates circadian rhythms. Molecular Cell.
66(4), 447–457.e7.
mla: Gustafson, Chelsea L., et al. “A Slow Conformational Switch in the BMAL1 Transactivation
Domain Modulates Circadian Rhythms.” Molecular Cell, vol. 66, no. 4, Elsevier,
2017, p. 447–457.e7, doi:10.1016/j.molcel.2017.04.011.
short: C.L. Gustafson, N.C. Parsley, H. Asimgil, H.-W. Lee, C. Ahlbach, A.K. Michael,
H. Xu, O.L. Williams, T.L. Davis, A.C. Liu, C.L. Partch, Molecular Cell 66 (2017)
447–457.e7.
date_created: 2024-03-21T07:56:01Z
date_published: 2017-05-18T00:00:00Z
date_updated: 2024-03-25T12:19:20Z
day: '18'
doi: 10.1016/j.molcel.2017.04.011
extern: '1'
intvolume: ' 66'
issue: '4'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.molcel.2017.04.011
month: '05'
oa: 1
oa_version: Published Version
page: 447-457.e7
publication: Molecular Cell
publication_identifier:
issn:
- 1097-2765
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: A slow conformational switch in the BMAL1 transactivation domain modulates
circadian rhythms
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 66
year: '2017'
...
---
_id: '15156'
abstract:
- lang: eng
text: Circadian clocks are ubiquitous timing systems that induce rhythms of biological
activities in synchrony with night and day. In cyanobacteria, timing is generated
by a posttranslational clock consisting of KaiA, KaiB, and KaiC proteins and a
set of output signaling proteins, SasA and CikA, which transduce this rhythm to
control gene expression. Here, we describe crystal and nuclear magnetic resonance
structures of KaiB-KaiC,KaiA-KaiB-KaiC, and CikA-KaiB complexes. They reveal how
the metamorphic properties of KaiB, a protein that adopts two distinct folds,
and the post–adenosine triphosphate hydrolysis state of KaiC create a hub around
which nighttime signaling events revolve, including inactivation of KaiA and reciprocal
regulation of the mutually antagonistic signaling proteins, SasA and CikA.
article_processing_charge: No
article_type: original
author:
- first_name: Roger
full_name: Tseng, Roger
last_name: Tseng
- first_name: Nicolette F.
full_name: Goularte, Nicolette F.
last_name: Goularte
- first_name: Archana
full_name: Chavan, Archana
last_name: Chavan
- first_name: Jansen
full_name: Luu, Jansen
last_name: Luu
- first_name: Susan E.
full_name: Cohen, Susan E.
last_name: Cohen
- first_name: Yong-Gang
full_name: Chang, Yong-Gang
last_name: Chang
- first_name: Joel
full_name: Heisler, Joel
last_name: Heisler
- first_name: Sheng
full_name: Li, Sheng
last_name: Li
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Sarvind
full_name: Tripathi, Sarvind
last_name: Tripathi
- first_name: Susan S.
full_name: Golden, Susan S.
last_name: Golden
- first_name: Andy
full_name: LiWang, Andy
last_name: LiWang
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Tseng R, Goularte NF, Chavan A, et al. Structural basis of the day-night transition
in a bacterial circadian clock. Science. 2017;355(6330):1174-1180. doi:10.1126/science.aag2516
apa: Tseng, R., Goularte, N. F., Chavan, A., Luu, J., Cohen, S. E., Chang, Y.-G.,
… Partch, C. L. (2017). Structural basis of the day-night transition in a bacterial
circadian clock. Science. American Association for the Advancement of Science.
https://doi.org/10.1126/science.aag2516
chicago: Tseng, Roger, Nicolette F. Goularte, Archana Chavan, Jansen Luu, Susan
E. Cohen, Yong-Gang Chang, Joel Heisler, et al. “Structural Basis of the Day-Night
Transition in a Bacterial Circadian Clock.” Science. American Association
for the Advancement of Science, 2017. https://doi.org/10.1126/science.aag2516.
ieee: R. Tseng et al., “Structural basis of the day-night transition in a
bacterial circadian clock,” Science, vol. 355, no. 6330. American Association
for the Advancement of Science, pp. 1174–1180, 2017.
ista: Tseng R, Goularte NF, Chavan A, Luu J, Cohen SE, Chang Y-G, Heisler J, Li
S, Michael AK, Tripathi S, Golden SS, LiWang A, Partch CL. 2017. Structural basis
of the day-night transition in a bacterial circadian clock. Science. 355(6330),
1174–1180.
mla: Tseng, Roger, et al. “Structural Basis of the Day-Night Transition in a Bacterial
Circadian Clock.” Science, vol. 355, no. 6330, American Association for
the Advancement of Science, 2017, pp. 1174–80, doi:10.1126/science.aag2516.
short: R. Tseng, N.F. Goularte, A. Chavan, J. Luu, S.E. Cohen, Y.-G. Chang, J. Heisler,
S. Li, A.K. Michael, S. Tripathi, S.S. Golden, A. LiWang, C.L. Partch, Science
355 (2017) 1174–1180.
date_created: 2024-03-21T07:56:24Z
date_published: 2017-03-17T00:00:00Z
date_updated: 2024-03-25T12:16:44Z
day: '17'
doi: 10.1126/science.aag2516
extern: '1'
intvolume: ' 355'
issue: '6330'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '03'
oa_version: None
page: 1174-1180
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structural basis of the day-night transition in a bacterial circadian clock
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 355
year: '2017'
...
---
_id: '15157'
abstract:
- lang: eng
text: The basic helix–loop–helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1
(brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian
transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity
by coactivators and repressors establishes the ∼24-h periodicity of gene expression.
Formation of a repressive complex, defined by the core clock proteins cryptochrome
1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression
to activation each day. Here we show that CRY1 binds directly to the PAS domain
core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain.
Integrative modeling and solution X-ray scattering studies unambiguously position
a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous
to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription
factor alongside the PAS domains, extending above the DNA-binding bHLH domain.
Single point mutations at the interface on either CRY1 or CLOCK disrupt formation
of the ternary complex, highlighting the importance of this interface for direct
regulation of CLOCK:BMAL1 activity by CRY1.
article_processing_charge: No
article_type: original
author:
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Jennifer L.
full_name: Fribourgh, Jennifer L.
last_name: Fribourgh
- first_name: Yogarany
full_name: Chelliah, Yogarany
last_name: Chelliah
- first_name: Colby R.
full_name: Sandate, Colby R.
last_name: Sandate
- first_name: Greg L.
full_name: Hura, Greg L.
last_name: Hura
- first_name: Dina
full_name: Schneidman-Duhovny, Dina
last_name: Schneidman-Duhovny
- first_name: Sarvind M.
full_name: Tripathi, Sarvind M.
last_name: Tripathi
- first_name: Joseph S.
full_name: Takahashi, Joseph S.
last_name: Takahashi
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: Michael AK, Fribourgh JL, Chelliah Y, et al. Formation of a repressive complex
in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Proceedings of the National Academy of Sciences. 2017;114(7):1560-1565.
doi:10.1073/pnas.1615310114
apa: Michael, A. K., Fribourgh, J. L., Chelliah, Y., Sandate, C. R., Hura, G. L.,
Schneidman-Duhovny, D., … Partch, C. L. (2017). Formation of a repressive complex
in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Proceedings of the National Academy of Sciences. Proceedings of the National
Academy of Sciences. https://doi.org/10.1073/pnas.1615310114
chicago: Michael, Alicia K., Jennifer L. Fribourgh, Yogarany Chelliah, Colby R.
Sandate, Greg L. Hura, Dina Schneidman-Duhovny, Sarvind M. Tripathi, Joseph S.
Takahashi, and Carrie L. Partch. “Formation of a Repressive Complex in the Mammalian
Circadian Clock Is Mediated by the Secondary Pocket of CRY1.” Proceedings of
the National Academy of Sciences. Proceedings of the National Academy of Sciences,
2017. https://doi.org/10.1073/pnas.1615310114.
ieee: A. K. Michael et al., “Formation of a repressive complex in the mammalian
circadian clock is mediated by the secondary pocket of CRY1,” Proceedings of
the National Academy of Sciences, vol. 114, no. 7. Proceedings of the National
Academy of Sciences, pp. 1560–1565, 2017.
ista: Michael AK, Fribourgh JL, Chelliah Y, Sandate CR, Hura GL, Schneidman-Duhovny
D, Tripathi SM, Takahashi JS, Partch CL. 2017. Formation of a repressive complex
in the mammalian circadian clock is mediated by the secondary pocket of CRY1.
Proceedings of the National Academy of Sciences. 114(7), 1560–1565.
mla: Michael, Alicia K., et al. “Formation of a Repressive Complex in the Mammalian
Circadian Clock Is Mediated by the Secondary Pocket of CRY1.” Proceedings of
the National Academy of Sciences, vol. 114, no. 7, Proceedings of the National
Academy of Sciences, 2017, pp. 1560–65, doi:10.1073/pnas.1615310114.
short: A.K. Michael, J.L. Fribourgh, Y. Chelliah, C.R. Sandate, G.L. Hura, D. Schneidman-Duhovny,
S.M. Tripathi, J.S. Takahashi, C.L. Partch, Proceedings of the National Academy
of Sciences 114 (2017) 1560–1565.
date_created: 2024-03-21T07:56:50Z
date_published: 2017-01-31T00:00:00Z
date_updated: 2024-03-25T12:12:23Z
day: '31'
doi: 10.1073/pnas.1615310114
extern: '1'
external_id:
pmid:
- '28143926'
intvolume: ' 114'
issue: '7'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1615310114
month: '01'
oa: 1
oa_version: Published Version
page: 1560-1565
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Formation of a repressive complex in the mammalian circadian clock is mediated
by the secondary pocket of CRY1
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 114
year: '2017'
...
---
_id: '15158'
abstract:
- lang: eng
text: 'Cryptochromes are evolutionarily related to the light‐dependent DNA repair
enzyme photolyase, serving as major regulators of circadian rhythms in insects
and vertebrate animals. There are two types of cryptochromes in the animal kingdom:
Drosophila‐like CRYs that act as nonvisual photopigments
linking circadian rhythms to the environmental light/dark cycle, and vertebrate‐like
CRYs that do not appear to sense light directly, but control the generation of
circadian rhythms by acting as transcriptional repressors. Some animals have both
types of CRYs, while others possess only one. Cryptochromes have two domains,
the photolyase homology region (PHR) and an extended, intrinsically disordered
C‐terminus. While all animal CRYs share a high degree of sequence and structural
homology in their PHR domains, the C‐termini are divergent in both length and
sequence identity. Recently, cryptochrome function has been shown to extend beyond
its pivotal role in circadian clocks, participating in regulation of the DNA damage
response, cancer progression and glucocorticoid signaling, as well as being implicated
as possible magnetoreceptors. In this review, we provide a historical perspective
on the discovery of animal cryptochromes, examine similarities and differences
of the two types of animal cryptochromes and explore some of the divergent roles
for this class of proteins.'
article_processing_charge: No
article_type: original
author:
- first_name: Alicia Kathleen
full_name: Michael, Alicia Kathleen
id: 6437c950-2a03-11ee-914d-d6476dd7b75c
last_name: Michael
- first_name: Jennifer L.
full_name: Fribourgh, Jennifer L.
last_name: Fribourgh
- first_name: Russell N.
full_name: Van Gelder, Russell N.
last_name: Van Gelder
- first_name: Carrie L.
full_name: Partch, Carrie L.
last_name: Partch
citation:
ama: 'Michael AK, Fribourgh JL, Van Gelder RN, Partch CL. Animal cryptochromes:
Divergent roles in light perception, circadian timekeeping and beyond. Photochemistry
and Photobiology. 2017;93(1):128-140. doi:10.1111/php.12677'
apa: 'Michael, A. K., Fribourgh, J. L., Van Gelder, R. N., & Partch, C. L. (2017).
Animal cryptochromes: Divergent roles in light perception, circadian timekeeping
and beyond. Photochemistry and Photobiology. Wiley. https://doi.org/10.1111/php.12677'
chicago: 'Michael, Alicia K., Jennifer L. Fribourgh, Russell N. Van Gelder, and
Carrie L. Partch. “Animal Cryptochromes: Divergent Roles in Light Perception,
Circadian Timekeeping and Beyond.” Photochemistry and Photobiology. Wiley,
2017. https://doi.org/10.1111/php.12677.'
ieee: 'A. K. Michael, J. L. Fribourgh, R. N. Van Gelder, and C. L. Partch, “Animal
cryptochromes: Divergent roles in light perception, circadian timekeeping and
beyond,” Photochemistry and Photobiology, vol. 93, no. 1. Wiley, pp. 128–140,
2017.'
ista: 'Michael AK, Fribourgh JL, Van Gelder RN, Partch CL. 2017. Animal cryptochromes:
Divergent roles in light perception, circadian timekeeping and beyond. Photochemistry
and Photobiology. 93(1), 128–140.'
mla: 'Michael, Alicia K., et al. “Animal Cryptochromes: Divergent Roles in Light
Perception, Circadian Timekeeping and Beyond.” Photochemistry and Photobiology,
vol. 93, no. 1, Wiley, 2017, pp. 128–40, doi:10.1111/php.12677.'
short: A.K. Michael, J.L. Fribourgh, R.N. Van Gelder, C.L. Partch, Photochemistry
and Photobiology 93 (2017) 128–140.
date_created: 2024-03-21T07:57:18Z
date_published: 2017-02-01T00:00:00Z
date_updated: 2024-03-25T12:09:21Z
day: '01'
doi: 10.1111/php.12677
extern: '1'
intvolume: ' 93'
issue: '1'
keyword:
- Physical and Theoretical Chemistry
- General Medicine
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/php.12677
month: '02'
oa: 1
oa_version: Published Version
page: 128-140
publication: Photochemistry and Photobiology
publication_identifier:
eissn:
- 1751-1097
issn:
- 0031-8655
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Animal cryptochromes: Divergent roles in light perception, circadian timekeeping
and beyond'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 93
year: '2017'
...
---
_id: '15239'
abstract:
- lang: eng
text: Using images from the Hubble Space Telescope Advanced Camera for Surveys,
we measure the rate of cooling of white dwarfs in the globular cluster 47 Tucanae
and compare it to modelled cooling curves. We examine the effects of the outer
convective envelope reaching the nearly isothermal degenerate core and the release
of latent heat during core crystallization on the white dwarf cooling rates. For
white dwarfs typical of 47 Tuc, the onset of these effects occur at similar times.
The latent heat released during crystallization is a small heat source. In contrast,
the heat reservoir of the degenerate core is substantially larger. When the convective
envelope reaches the nearly isothermal interior of the white dwarf, the star becomes
brighter than it would be in the absence of this effect. Our modelled cooling
curves that include this convective coupling closely match the observed luminosity
function of the white dwarfs in 47 Tuc.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Alysa
full_name: Obertas, Alysa
last_name: Obertas
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: Jeremy
full_name: Heyl, Jeremy
last_name: Heyl
- first_name: Harvey
full_name: Richer, Harvey
last_name: Richer
- first_name: Jason
full_name: Kalirai, Jason
last_name: Kalirai
- first_name: Pier-Emmanuel
full_name: Tremblay, Pier-Emmanuel
last_name: Tremblay
citation:
ama: Obertas A, Caiazzo I, Heyl J, Richer H, Kalirai J, Tremblay P-E. The onset
of convective coupling and freezing in the white dwarfs of 47 Tucanae. Monthly
Notices of the Royal Astronomical Society. 2017;474(1):677-682. doi:10.1093/mnras/stx2759
apa: Obertas, A., Caiazzo, I., Heyl, J., Richer, H., Kalirai, J., & Tremblay,
P.-E. (2017). The onset of convective coupling and freezing in the white dwarfs
of 47 Tucanae. Monthly Notices of the Royal Astronomical Society. Oxford
University Press. https://doi.org/10.1093/mnras/stx2759
chicago: Obertas, Alysa, Ilaria Caiazzo, Jeremy Heyl, Harvey Richer, Jason Kalirai,
and Pier-Emmanuel Tremblay. “The Onset of Convective Coupling and Freezing in
the White Dwarfs of 47 Tucanae.” Monthly Notices of the Royal Astronomical
Society. Oxford University Press, 2017. https://doi.org/10.1093/mnras/stx2759.
ieee: A. Obertas, I. Caiazzo, J. Heyl, H. Richer, J. Kalirai, and P.-E. Tremblay,
“The onset of convective coupling and freezing in the white dwarfs of 47 Tucanae,”
Monthly Notices of the Royal Astronomical Society, vol. 474, no. 1. Oxford
University Press, pp. 677–682, 2017.
ista: Obertas A, Caiazzo I, Heyl J, Richer H, Kalirai J, Tremblay P-E. 2017. The
onset of convective coupling and freezing in the white dwarfs of 47 Tucanae. Monthly
Notices of the Royal Astronomical Society. 474(1), 677–682.
mla: Obertas, Alysa, et al. “The Onset of Convective Coupling and Freezing in the
White Dwarfs of 47 Tucanae.” Monthly Notices of the Royal Astronomical Society,
vol. 474, no. 1, Oxford University Press, 2017, pp. 677–82, doi:10.1093/mnras/stx2759.
short: A. Obertas, I. Caiazzo, J. Heyl, H. Richer, J. Kalirai, P.-E. Tremblay, Monthly
Notices of the Royal Astronomical Society 474 (2017) 677–682.
date_created: 2024-03-26T10:40:05Z
date_published: 2017-10-24T00:00:00Z
date_updated: 2024-04-08T07:04:10Z
day: '24'
doi: 10.1093/mnras/stx2759
extern: '1'
external_id:
arxiv:
- '1709.08097'
intvolume: ' 474'
issue: '1'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1709.08097
month: '10'
oa: 1
oa_version: Preprint
page: 677-682
publication: Monthly Notices of the Royal Astronomical Society
publication_identifier:
eissn:
- 1365-2966
issn:
- 0035-8711
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The onset of convective coupling and freezing in the white dwarfs of 47 Tucanae
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 474
year: '2017'
...
---
_id: '15240'
abstract:
- lang: eng
text: "Multi-epoch observations with the Advanced Camera Survey and WFC3 on the
Hubble Space Telescope provide a unique and comprehensive probe of stellar dynamics
within 47 Tucanae. We confront analytic models of the globular cluster with the
observed stellar proper motions that probe along the main sequence from just above
0.8–0.1M⊙ as well as white dwarfs younger than 1 Gyr. One field lies just beyond
the half-light radius where dynamical models (e.g., lowered Maxwellian distributions)
make robust predictions for the stellar proper motions. The observed proper motions
in this outer field show evidence for anisotropy in the velocity distribution
as well as skewness; the latter is evidence of rotation. The measured velocity
dispersions and surface brightness distributions agree in detail with a rotating
anisotropic model of the stellar distribution function with mild dependence of
the proper-motion dispersion on mass. However, the best-fitting models underpredict
the rotation and skewness of the stellar velocities. In the second field, centered
on the core of the cluster, the mass segregation in proper motion is much stronger.
Nevertheless the model developed in the outer field can be extended inward by
taking this mass segregation into account in a heuristic fashion. The proper motions
of the main-sequence stars yield a mass estimate of the cluster of \r\n at a distance
of 4.7 kpc. By comparing the proper motions of a sample of giant and subgiant
stars with the observed radial velocities we estimate the distance to the cluster
kinematically to be 4.29 ± 0.47 kpc."
article_number: '186'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: J.
full_name: Heyl, J.
last_name: Heyl
- first_name: Ilaria
full_name: Caiazzo, Ilaria
id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d
last_name: Caiazzo
orcid: 0000-0002-4770-5388
- first_name: H.
full_name: Richer, H.
last_name: Richer
- first_name: J.
full_name: Anderson, J.
last_name: Anderson
- first_name: J.
full_name: Kalirai, J.
last_name: Kalirai
- first_name: J.
full_name: Parada, J.
last_name: Parada
citation:
ama: 'Heyl J, Caiazzo I, Richer H, Anderson J, Kalirai J, Parada J. Deep HST imaging
in 47 Tucanae: A global dynamical model. The Astrophysical Journal. 2017;850(2).
doi:10.3847/1538-4357/aa974f'
apa: 'Heyl, J., Caiazzo, I., Richer, H., Anderson, J., Kalirai, J., & Parada,
J. (2017). Deep HST imaging in 47 Tucanae: A global dynamical model. The Astrophysical
Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/aa974f'
chicago: 'Heyl, J., Ilaria Caiazzo, H. Richer, J. Anderson, J. Kalirai, and J. Parada.
“Deep HST Imaging in 47 Tucanae: A Global Dynamical Model.” The Astrophysical
Journal. American Astronomical Society, 2017. https://doi.org/10.3847/1538-4357/aa974f.'
ieee: 'J. Heyl, I. Caiazzo, H. Richer, J. Anderson, J. Kalirai, and J. Parada, “Deep
HST imaging in 47 Tucanae: A global dynamical model,” The Astrophysical Journal,
vol. 850, no. 2. American Astronomical Society, 2017.'
ista: 'Heyl J, Caiazzo I, Richer H, Anderson J, Kalirai J, Parada J. 2017. Deep
HST imaging in 47 Tucanae: A global dynamical model. The Astrophysical Journal.
850(2), 186.'
mla: 'Heyl, J., et al. “Deep HST Imaging in 47 Tucanae: A Global Dynamical Model.”
The Astrophysical Journal, vol. 850, no. 2, 186, American Astronomical
Society, 2017, doi:10.3847/1538-4357/aa974f.'
short: J. Heyl, I. Caiazzo, H. Richer, J. Anderson, J. Kalirai, J. Parada, The Astrophysical
Journal 850 (2017).
date_created: 2024-03-26T10:40:23Z
date_published: 2017-12-01T00:00:00Z
date_updated: 2024-04-08T07:04:35Z
day: '01'
doi: 10.3847/1538-4357/aa974f
extern: '1'
external_id:
arxiv:
- '1710.10666'
intvolume: ' 850'
issue: '2'
keyword:
- Space and Planetary Science
- Astronomy and Astrophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.1710.10666
month: '12'
oa: 1
oa_version: Preprint
publication: The Astrophysical Journal
publication_identifier:
eissn:
- 1538-4357
issn:
- 0004-637X
publication_status: published
publisher: American Astronomical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Deep HST imaging in 47 Tucanae: A global dynamical model'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 850
year: '2017'
...